Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_011764111.1 AZO_RS01895 ornithine--oxo-acid transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000061505.1:WP_011764111.1 Length = 706 Score = 274 bits (701), Expect = 5e-78 Identities = 164/398 (41%), Positives = 225/398 (56%), Gaps = 15/398 (3%) Query: 4 RELIDKYHMNTYSRFPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKE 63 RE ++ Y+ PV GEG +WD EG Y+D+++ + GH +P ++ A+++ Sbjct: 311 REKERRFGATNYAPMPVVFHRGEGVWLWDVEGTRYLDMMSAYSAVSFGHANPRLLRALQD 370 Query: 64 QVERLIHCSNLYYNEPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGCTK 123 Q + L S + N+ L + N+G E+VE A+K ARK+ K Sbjct: 371 QAQLLTLTSRSFSNDRLPLLLERLCSLL--GFERALPVNTGLEAVETALKAARKWAYIVK 428 Query: 124 --------FIAFEGGFHGRTMGALSATWKPEFREPFEPLVPEFEHVPYGDVNAVEKAIDD 175 IA EG FHGR++ + + K ++R+ F P P VP+GD A+E AI Sbjct: 429 GVPPDRAEIIACEGNFHGRSITIVGLSSKEQYRDGFGPFPPGLRRVPFGDPTALEAAITP 488 Query: 176 DTAAVIVEPVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHED 235 TAA +VEP+QGE G+ +PP G+L E+C H +LLI DEVQ+G+GRTG+ A +H+ Sbjct: 489 HTAAFLVEPIQGEGGIIVPPPGYLAHCAEICRRHNVLLIADEVQTGLGRTGRLLACDHDG 548 Query: 236 VLPDIVCLAKGLGGG-VPVGATIAREEVAEAFEPGDHGSTFGGNPLACAAVCAAVSTVLE 294 V PD + L K LGGG +PV A +A EV + F PGDHGSTFGGNPL AAV V +L Sbjct: 549 VRPDGLILGKALGGGLLPVSAFLADREVMDVFRPGDHGSTFGGNPLG-AAVALEVLDLLA 607 Query: 295 ENLP-EAAERKGKLAMRILSEAE-DVVEEVRGRGLMMGVEVGDDER-AKDVAREMLDRGA 351 E P EAAER G+ L AE V EVRGRGL++GV + + A+ VA +L RG Sbjct: 608 ETRPWEAAERLGRRLRAELEAAELPCVREVRGRGLLIGVALDPVKAPAQLVAELLLARGI 667 Query: 352 LVNVTSGDVIRLVPPLVIGEDELEKALAELADALRASG 389 T+G+VIRL PPL I E L++A A + D L G Sbjct: 668 ATRDTNGNVIRLAPPLTIDEGTLDRAAAIIIDTLNPLG 705 Lambda K H 0.318 0.137 0.405 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 722 Number of extensions: 49 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 389 Length of database: 706 Length adjustment: 35 Effective length of query: 354 Effective length of database: 671 Effective search space: 237534 Effective search space used: 237534 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory